Genetically Encoded Fragment-Based Drug Discovery Project Summary The ultimate goal of this project is to develop a new approach for discovering small molecules against intractable protein-protein interaction (PPI) interfaces that are difficult to address using current fragment-based library approaches. Our strategy involves reengineering ribosomal translation to encode libraries of diverse pharmacophore side chains embedded in known protein structures. This approach will allow rapid searches of large chemical space with exquisitely controlled resolution in order to find drug leads more rapidly and with less expense. The experimental approach is based on well validated cell-free synthesis of proteins. The principle aims are to (i) develop chemical and biochemical methods of fragment library assembly (ii) design, build, and test an in vitro ribosomal 'chassis'for genetic encoding of fragment-based libraries, and (iii) identify novel pharmacophore structures presented on alpha-helical proteins that will be able to affect a PPI. The first demonstration protein studied, Bcl-2, is a validated target for anti-cancer agents, and will therefore lead to development of new drugs. Successful completion of this project would demonstrate a platform technology that could produce unprecedented improvements in our ability to modulate PPIs across multiple target classes and diseases with small molecule ligands.
Protein-protein interactions are misregulated in human diseases such as cancer and therefore represent compelling but challenging targets for therapeutic intervention with small molecule drugs. These challenges could be overcome by genetically encoding chemical structures into proteins in order to identify possible small molecule inhibitors of these interactions. This approach integrates the complementary strengths of both protein engineering and small molecule drug design for discovery of new therapeutics to treat human diseases.